The present disclosure relates generally to cancer diagnostics and in particular to a diagnostic tool for determining a cancer type from DNA sequence data using a library of cancer genomic signatures.
Cancer is a disease resulting from uncontrolled and abnormal cell growth. It is currently understood that non-hereditary cancer results from somatic mutations in an individual's DNA. Different somatic mutations give rise to different types of cancer. Different types of cancer may be distinguished based on the organ or tissue of origin. In some cases, modern clinical and molecular pathology techniques support distinguishing multiple different subtypes of cancer affecting a given organ or tissue (e.g., hepatocellular carcinoma, intrahepatic bile duct carcinoma and hepatoblastoma are some of the currently known liver cancer subtypes). As used herein, the term “cancer type” may refer to a type of cancer (based on organ or tissue of origin) or a cancer subtype (for an organ or tissue). (Hereinafter, the term “organ” may refer to an organ or tissue, as applicable.) At present, the relationship between a particular somatic mutation and a particular cancer type is not well understood, although mutations in a few specific genes have been associated with particular cancer types.
Different types of cancer respond better to different treatment options. Thus, knowing the type of cancer a patient has is crucial to developing an optimal treatment plan. Further, cancer is a progressive disease, and early detection increases the prospects for successful treatment.
At present, the most common technique for detecting and diagnosing cancer begins with detecting a tumor, e.g., by tactile examination, visual inspection, and/or medical imaging. Once a tumor is detected, a biopsy can be performed. (As used herein, the term “biopsy” refers to a standard tumor biopsy where tissue or cell samples are taken.) During a biopsy, a medical professional extracts a tissue sample from the tumor area. This sample may be analyzed to determine whether it is cancerous and, if so, the type of cancer. A biopsy is typically an invasive and unpleasant procedure for a patient to endure, and like all invasive procedures, biopsy has medical risks. In addition, a biopsy is only useful after a tumor has become detectable; earlier detection may be desirable.
Currently, techniques are being developed to analyze cell-free DNA (cfDNA) extracted from a sample of a patient's blood in order to detect molecular abnormalities within the cfDNA population. A subpopulation of cfDNA with such abnormalities, referred to as circulating tumor DNA, or ctDNA, may be indicative of the presence of cancer in the tested patient. Such a procedure would be less invasive than a biopsy and may also support earlier detection of cancer. However, since blood circulates throughout the body, merely detecting indicia of cancer from a blood sample may not be sufficient information for developing a treatment plan. It is still necessary to identify the type of cancer, including the organ of origin. Thus, a blood test that merely indicates the patient has cancer would be of limited use. Further improvements are desirable.